Domingo "Jokemaster" Chavo: My starting character, who's been negelected lately. He joined the rebels near the end of the civil war, then became a mercenary. Most of his jobs came from the NRI. Greer hired him for very dangerous missions which officially the NRI couldn't do.
Jim Greer: A veteran intelligence agent, he joined the rebellion at the height of the Civil War. He was a teenager at the time. Since then he's fought for what he thought was right. He is currently in the new rebellion along with his team.
O'Conner, Price, Deiter, Dominguez: Snipers on Greer's team.
Perez: Tech wiz on Greer's team.
Caruso, Clark: Soldiers on Greer's team.
Spook: A random spec ops agent stuck on Duriel.))
*Greer nods at the rest and they leave the room*
Vader's wife was very pregnant when she died 19 years ago. All of a sudden a 19 year old who is very strong in the force and has a distinct resembalance to him in his younger days rolls in from Vader's home planet with his old Master Obi-Wan (Who was the ONLY other person preset at the time his wife died. And to boot, the kid's last name is Skywalker.
So in answer to your question, he knew Luke was his son because his name is Darth Vader, and not Darth Retard.
-Forum post on why Vader knew Luke was his son.